SAXSdb — 9ckx

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 165–234 Chain B； UniProt 165–234	Mutation：I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；2.5% MPD, 100 mM Tris pH 8.5	Resolution 1.98 Å R-free 0.232

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1A0HF11_9ASCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–74； UniProt 165–234 Author chain B； PDBConstruct 5–74； UniProt 165–234

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

Homo sapiens

UniProt A0AA46P9Z6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–124 Chain B； UniProt 2–124	Mutation：I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；2.5% MPD, 100 mM Tris pH 8.5	Resolution 1.98 Å R-free 0.232

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0AA46P9Z6_MYXXA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 77–199； UniProt 2–124 Author chain B； PDBConstruct 77–199； UniProt 2–124

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

Homo sapiens

UniProt P63027

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 95–114 Chain B； UniProt 95–114	Mutation：I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；2.5% MPD, 100 mM Tris pH 8.5	Resolution 1.98 Å R-free 0.232

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9CKX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) Deposited 2008-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 22–58（37 aa） Fragment：residues 22-58	Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) Deposited 2008-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 22–58（37 aa） Fragment：residues 22-58	Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3FII Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh2) Deposited 2008-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–53（32 aa） Fragment：residues 27-58	Mutation：Q58DCY Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.17 Å R-free 0.290
3RK2 Truncated SNARE complex Deposited 2011-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K	Resolution 2.20 Å R-free 0.268
3RK2 Truncated SNARE complex Deposited 2011-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；294 K；0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K	Resolution 2.20 Å R-free 0.268
3RK3 Truncated SNARE complex with complexin Deposited 2011-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.50 Å R-free 0.316
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain M 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain Q 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain U 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain Y 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
3RL0 Truncated SNARE complex with complexin (P1) Deposited 2011-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain c 28–60（33 aa） Fragment：UNP residues 28-60	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；13-15% polyethyleneglycol (PEG) 5000MME, 0.2 M ammonium sulfate, 0.01 M EDTA, and 0.1 M Tris pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 3.80 Å R-free 0.345
7UDC cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 29–83（55 aa）	Mutation：Q36C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VAMP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 203–222； UniProt 95–114 Author chain B； PDBConstruct 203–222； UniProt 95–114

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ckx
Deposition date deposition_date	2024-07-10
Structure title title	Crystal structure of Dsk2 Sti1 domain bound to a transmembrane domain
Keywords keywords	Membrane protein Chaperone Sti1 Ubiquilin, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.77 Å
Radius of gyration Rg (electron density) rg_electron	25.05 Å
Forward intensity I(0) i0	41862300.00
Molecular weight molecular_weight	48741.0 kDa
Excluded volume excluded_volume	60611 Å³
Envelope volume envelope_volume	73972 Å³
Hydration-shell volume shell_volume	25239 Å³
Envelope diameter envelope_diameter	81.4 Å
Shell Rg shell_rg	31.73 Å
Envelope Rg envelope_rg	25.14 Å
Shape Rg shape_rg	25.09 Å
Total Rg total_rg	25.66 Å
Total atoms total_atoms	6830
Residues n_residues	444
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	25.72 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	4.1860e+07
I(0) uncertainty (real space) i0_real_error	5.4700e+05
Rg (reciprocal space) rg_reciprocal	25.74 Å
I(0) (reciprocal space) i0_reciprocal	41860000.0000
Solution quality estimate total_estimate	0.9109
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.729
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14340000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	67.410 Å
Unit-cell length b length_b	63.920 Å
Unit-cell length c length_c	67.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	46.130 Å
R factor r_factor	0.2207
R_work r_work	0.2200
R_free r_free	0.2321

Description description	Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2
Molecular weight formula_weight	24419.4 kDa
Mutation mutation	I98A,I102A,I106A,I108A,I110A,I111A (Uniprot Vamp2 numbering) in the Vamp2 segment
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6954

Crystal structure of Dsk2 Sti1 domain bound to a transmembrane domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

fit	/app/data/saxs_computation/ck/9ckx/9ckx.fit
pddf	/app/data/pr_computation/ck/9ckx/9ckx.pr.out
profile	/app/data/saxs_computation/ck/9ckx/9ckx.dat